There are a lot of settings saved when qGo is getting closed. Thus, by running several instances of qGo the last closed instance of qGo supersedes the settings.
This is different to closing a board window since all board settings are updated simultaneosly and they are saved when qGo quits.
When the command line on the lower side has focus, i.e. after pressing Escape or clicking onto the command line, the window position and size can rapidly be changed by pressing CTRL + 0 .. 9 whereby the window position and size have to be saved once by pressing the same number ALT + 0 .. 9 before.